[1]} compared the marginal likelihoods of alternative
partitioning strategies (in combination with either strict or relaxed-clock
models) for an alignment of whole mitochondrial genomes of carnivores.
They used the harmonic mean, stabilized harmonic mean [2]},
path sampling, and stepping-stone estimators.
For all 41 models they evaluated, both harmonic mean estimators returned much
larger marginal likelihoods than path sampling and stepping stone, again
suggesting these estimators based solely on the posterior sample are unable to
adequately penalize the models.
They also found that by allowing the sharing of information among partitions
via hierarchical modeling [3]}, the model with the largest PS
and SS-estimated marginal likelihood switched from a codon model to a
nucleotide model partitioned by codon position.
This demonstrates the sensitivity of marginal likelihoods to prior assumptions.
